On the Linearization of Scaffolds Sharing Repeated Contigs - LIRMM - Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier Access content directly
Conference Papers Year : 2017

On the Linearization of Scaffolds Sharing Repeated Contigs

Abstract

Scaffolding is the final step in assembling Next Generation Sequencing data, in which pre-assembled contiguous regions (“contigs”) are oriented and ordered using information that links them (for example, mapping of paired-end reads). As the genome of some species is highly repetitive, we allow placing some contigs multiple times, thereby generalizing established computational models for this problem. We study the subsequent problems induced by the translation of solutions of the model back to actual sequences, proposing models and analyzing the complexity of the resulting computational problems. We find both polynomial-time and $NP$ -hard special cases like planarity or bounded degree.
No file

Dates and versions

lirmm-01672893 , version 1 (27-12-2017)

Identifiers

Cite

Mathias Weller, Annie Chateau, Rodolphe Giroudeau. On the Linearization of Scaffolds Sharing Repeated Contigs. COCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.509-517, ⟨10.1007/978-3-319-71147-8_38⟩. ⟨lirmm-01672893⟩
218 View
0 Download

Altmetric

Share

Gmail Facebook X LinkedIn More